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Results: 1 to 20 of 48

1.

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.

Wei GH, Badis G, Berger MF, Kivioja T, Palin K, Enge M, Bonke M, Jolma A, Varjosalo M, Gehrke AR, Yan J, Talukder S, Turunen M, Taipale M, Stunnenberg HG, Ukkonen E, Hughes TR, Bulyk ML, Taipale J.

EMBO J. 2010 Jul 7;29(13):2147-60. doi: 10.1038/emboj.2010.106. Epub 2010 Jun 1.

PMID:
20517297
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Inferring binding energies from selected binding sites.

Zhao Y, Granas D, Stormo GD.

PLoS Comput Biol. 2009 Dec;5(12):e1000590. doi: 10.1371/journal.pcbi.1000590. Epub 2009 Dec 4.

PMID:
19997485
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Bind-n-Seq: high-throughput analysis of in vitro protein-DNA interactions using massively parallel sequencing.

Zykovich A, Korf I, Segal DJ.

Nucleic Acids Res. 2009 Dec;37(22):e151. doi: 10.1093/nar/gkp802. Epub .

PMID:
19843614
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer.

Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, Beckwith CA, Chan JA, Hills A, Davis M, Yao K, Kehoe SM, Lenz HJ, Haiman CA, Yan C, Henderson BE, Frenkel B, Barretina J, Bass A, Tabernero J, Baselga J, Regan MM, Manak JR, Shivdasani R, Coetzee GA, Freedman ML.

Nat Genet. 2009 Aug;41(8):882-4. doi: 10.1038/ng.403. Epub 2009 Jun 28.

PMID:
19561607
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling.

Tuupanen S, Turunen M, Lehtonen R, Hallikas O, Vanharanta S, Kivioja T, Björklund M, Wei G, Yan J, Niittymäki I, Mecklin JP, Järvinen H, Ristimäki A, Di-Bernardo M, East P, Carvajal-Carmona L, Houlston RS, Tomlinson I, Palin K, Ukkonen E, Karhu A, Taipale J, Aaltonen LA.

Nat Genet. 2009 Aug;41(8):885-90. doi: 10.1038/ng.406. Epub 2009 Jun 28.

PMID:
19561604
[PubMed - indexed for MEDLINE]
6.

Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.

PMID:
19443739
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B.

Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.

PMID:
19295514
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.

Nat Rev Genet. 2009 Apr;10(4):252-63. doi: 10.1038/nrg2538.

PMID:
19274049
[PubMed - indexed for MEDLINE]
9.

Blimp-1/PRDM1 mediates transcriptional suppression of the NLR gene NLRP12/Monarch-1.

Lord CA, Savitsky D, Sitcheran R, Calame K, Wright JR, Ting JP, Williams KL.

J Immunol. 2009 Mar 1;182(5):2948-58. doi: 10.4049/jimmunol.0801692.

PMID:
19234190
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.

PMID:
19111667
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A dimer-specific function of the transcription factor NFATp.

Falvo JV, Lin CH, Tsytsykova AV, Hwang PK, Thanos D, Goldfeld AE, Maniatis T.

Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19637-42. doi: 10.1073/pnas.0810648105. Epub 2008 Dec 5.

PMID:
19060202
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Species-specific transcription in mice carrying human chromosome 21.

Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, Fisher EM, Tavaré S, Odom DT.

Science. 2008 Oct 17;322(5900):434-8. doi: 10.1126/science.1160930. Epub 2008 Sep 11.

PMID:
18787134
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ.

Genome Res. 2008 Dec;18(12):1906-17. doi: 10.1101/gr.078519.108. Epub 2008 Sep 11.

PMID:
18787082
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

PMID:
18714091
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.

PMID:
18585359
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6. Epub 2007 Nov 15.

PMID:
18006571
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Advances in SELEX and application of aptamers in the central nervous system.

Yang Y, Yang D, Schluesener HJ, Zhang Z.

Biomol Eng. 2007 Dec;24(6):583-92. Epub 2007 Jul 5. Review.

PMID:
17681489
[PubMed - indexed for MEDLINE]
18.

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S.

Nat Methods. 2007 Aug;4(8):651-7. Epub 2007 Jun 11.

PMID:
17558387
[PubMed - indexed for MEDLINE]
19.

Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands.

Hampshire AJ, Rusling DA, Broughton-Head VJ, Fox KR.

Methods. 2007 Jun;42(2):128-40. Review.

PMID:
17472895
[PubMed - indexed for MEDLINE]
20.

High-throughput assay for determining specificity and affinity of protein-DNA binding interactions.

Hallikas O, Taipale J.

Nat Protoc. 2006;1(1):215-22.

PMID:
17406235
[PubMed - indexed for MEDLINE]

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